MolNFT v1 · #153463 · protein
K4U bound crystal structure of class I type B peptide deformylase from acinetobacter baumannii
6JF8: “K4U bound crystal structure of class I type B peptide deformylase from acinetobacter baumannii”. X-ray diffraction, 2 ligands (LHY, ZN), 5 pockets (best druggability 0.70). MolNFT v1 #153463 on GenesisL1: 3D structure, binding sites…
- PDB
- 6JF8
- Type
- protein
- Length
- 634 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Peptide deformylase
- EC
- 3.5.1.88
- UniProt
- A0A0E1FIJ3
- Ligands
- LHY, ZN
- Pockets
- 5 · best druggability 0.70
Structure
x-ray diffraction · 3 distinct chains · 28% helix, 34% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Peptide deformylase (EC 3.5.1.88) | protein | 159 | 28% helix, 35% strand | A0A0E1FIJ3 |
| B | Peptide deformylase (EC 3.5.1.88) | protein | 158 | 28% helix, 32% strand | A0A0E1FIJ3 |
| D | Peptide deformylase (EC 3.5.1.88) | protein | 158 | 28% helix, 34% strand | A0A0E1FIJ3 |
Ligands and binding sites
- LHY · L-[(N-hydroxyamino)carbonyl]phenylalanine · ligand · 4 copies · chains A, B, C, D
- ZN · Zinc ion · metal · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 57 | 0.70 | 0.97 | 17 | LHY |
| 2 | 59 | 0.69 | 0.96 | 18 | ZN, LHY |
| 3 | 73 | 0.66 | 0.93 | 24 | LHY |
| 4 | 477 | 0.62 | 0.76 | 48 | empty |
| 5 | 87 | 0.59 | 0.88 | 26 | LHY |
Interfaces
3 interfaces between chains.
- C–D · 921 Ų buried · 4 hydrogen bonds · protein-protein
- A–B · 918 Ų buried · 4 hydrogen bonds · protein-protein
- B–C · 279 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 6JF8 · K4U bound crystal structure of class I type b peptide deformylase from Acinetobacter… · the same entry in another collection · chain A against A, TM-score 1.00
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt A0A0E1FIJ3
- Elsewhere: RCSB PDB 6JF8 · PDBe 6JF8 · UniProt A0A0E1FIJ3
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